Bco perms (#293)

* Add `DraftRetrieveApi`

To do this functions related to Prefixes and the associated permissions were created

Changes to be committed:
	modified:   biocompute/apis.py
	modified:   biocompute/models.py
	modified:   biocompute/selectors.py
	modified:   biocompute/services.py
	modified:   biocompute/urls.py
	modified:   config/asgi.py
	modified:   config/fixtures/local_data.json
	modified:   config/services.py
	modified:   config/urls.py
	modified:   prefix/selectors.py
	modified:   prefix/services.py
	deleted:    test.json
	modified:   tests/fixtures/example_bco.py
	modified:   tests/fixtures/test_data.json
	deleted:    token.json

* Update testing functions

Created subdirectory and moved test functions
Changes to be committed:
	renamed:    tests/test_views/__init__.py -> tests/test_apis/__init__.py
	new file:   tests/test_apis/test_api_authentication/__init__.py
	renamed:    tests/test_views/test_account_activate.py -> tests/test_apis/test_api_authentication/test_account_activate.py
	renamed:    tests/test_views/test_account_describe.py -> tests/test_apis/test_api_authentication/test_account_describe.py
	renamed:    tests/test_views/test_account_new.py -> tests/test_apis/test_api_authentication/test_account_new.py
	renamed:    tests/test_views/test_api_auth_add.py -> tests/test_apis/test_api_authentication/test_api_auth_add.py
	renamed:    tests/test_views/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/test_api_auth_remove.py
	renamed:    tests/test_views/test_api_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_views/test_api_objects_drafts_create.py -> tests/test_apis/test_api_objects_drafts_create.py
	renamed:    tests/test_views/test_auth_add.py -> tests/test_apis/test_auth_add.py
	renamed:    tests/test_views/test_auth_remove.py -> tests/test_apis/test_auth_remove.py
	renamed:    tests/test_views/test_auth_reset_token.py -> tests/test_apis/test_auth_reset_token.py
	renamed:    tests/test_views/test_objects_drafts_create.py -> tests/test_apis/test_objects_drafts_create.py
	renamed:    tests/test_views/test_prefixes_create.py -> tests/test_apis/test_prefixes_create.py
	new file:   tests/test_apis/test_prefixes_modify.py
	deleted:    tests/test_views/test_api_account_activate.py
	deleted:    tests/test_views/test_api_account_describe.py
	deleted:    tests/test_views/test_api_account_new.py
	deleted:    tests/test_views/test_prefixes_modify.py

* Update to Test functions

Changes to be committed:
	modified:   biocompute/migrations/0001_initial.py
	modified:   docs/refactor.md
	modified:   prefix/apis.py
	modified:   prefix/migrations/0001_initial.py
	modified:   prefix/services.py
	new file:   tests/fixtures/bco_dump.json
	modified:   tests/fixtures/test_data.json
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_add.py
	deleted:    tests/test_apis/test_api_authentication/test_api_auth_reset_token.py
	renamed:    tests/test_apis/test_auth_add.py -> tests/test_apis/test_api_authentication/test_auth_add.py
	renamed:    tests/test_apis/test_auth_reset_token.py -> tests/test_apis/test_api_authentication/test_auth_reset_token.py
	renamed:    tests/test_apis/test_api_authentication/test_api_auth_remove.py -> tests/test_apis/test_api_authentication/testi_auth_remove.py
	deleted:    tests/test_apis/test_api_objects_drafts_create.py
	new file:   tests/test_apis/test_api_prefix/__init__.py
	renamed:    tests/test_apis/test_prefixes_create.py -> tests/test_apis/test_api_prefix/test_prefixes_create.py
	renamed:    tests/test_apis/test_prefixes_modify.py -> tests/test_apis/test_api_prefix/test_prefixes_modify.py
	deleted:    tests/test_apis/test_auth_remove.py
	new file:   tests/test_apis/test_biocompute/__init__.py
	renamed:    tests/test_apis/test_objects_drafts_create.py -> tests/test_apis/test_biocompute/test_objects_drafts_create.py

Author: HadleyKing

biocompute/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 3.2.13 on 2024-03-20 18:48
+# Generated by Django 3.2.13 on 2024-04-02 20:08
 
 from django.conf import settings
 from django.db import migrations, models
@@ -10,9 +10,8 @@ class Migration(migrations.Migration):
     initial = True
 
     dependencies = [
-        ('prefix', '0001_initial'),
-        ('auth', '0012_alter_user_first_name_max_length'),
         migrations.swappable_dependency(settings.AUTH_USER_MODEL),
+        ('prefix', '0001_initial'),
     ]
 
     operations = [
@@ -24,9 +23,8 @@ class Migration(migrations.Migration):
                 ('state', models.CharField(choices=[('REFERENCED', 'referenced'), ('PUBLISHED', 'published'), ('DRAFT', 'draft'), ('DELETE', 'delete')], default='DRAFT', max_length=20)),
                 ('last_update', models.DateTimeField()),
                 ('access_count', models.IntegerField(default=0)),
-                ('authorized_groups', models.ManyToManyField(blank=True, to='auth.Group')),
                 ('authorized_users', models.ManyToManyField(blank=True, related_name='authorized_bcos', to=settings.AUTH_USER_MODEL)),
-                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='owned_bcos', to=settings.AUTH_USER_MODEL)),
+                ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='owned_bcos', to=settings.AUTH_USER_MODEL, to_field='username')),
                 ('prefix', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to='prefix.prefix')),
             ],
         ),

docs/refactor.md

@@ -52,4 +52,13 @@ Prefix Perms:
 	delete -> Delete Draft
 	publish -> Publish Draft
 	view -> View/download 
-   ONLY if private
+   ONLY if private
+   
+  If prefix is public anyone can view, but only auth users can modify.
+  
+  Things to look for when reviewing code:
+  - variable names are consistant and make sense
+  - all functions have documentation. This shoudl include:
+	- descriptions
+	- explicit parameters/inputs and outputs/returns
+	-  hoverover should display function documentation

prefix/apis.py

@@ -124,6 +124,8 @@ def post(self, request) -> Response:
         data = request.data
         rejected_requests = False
         accepted_requests = False
+        if 'POST_api_prefixes_create' in request.data:
+            data = legacy_api_converter(request.data)
 
         if data[0]['prefix']=='test' and data[0]['public'] is True:
             return Response(
@@ -132,9 +134,6 @@ def post(self, request) -> Response:
                     'TEST',"SUCCESS",201,"Prefix TEST created"
                 )
             )
-
-        if 'POST_api_prefixes_create' in request.data:
-            data = legacy_api_converter(request.data)
 
         for index, object in enumerate(data):
             response_id = object.get("prefix", index).upper()

prefix/migrations/0001_initial.py

@@ -1,4 +1,4 @@
-# Generated by Django 3.2.13 on 2024-03-20 18:48
+# Generated by Django 3.2.13 on 2024-04-02 20:08
 
 from django.conf import settings
 from django.db import migrations, models
@@ -12,7 +12,6 @@ class Migration(migrations.Migration):
 
     dependencies = [
         migrations.swappable_dependency(settings.AUTH_USER_MODEL),
-        ('auth', '0012_alter_user_first_name_max_length'),
     ]
 
     operations = [
@@ -24,7 +23,7 @@ class Migration(migrations.Migration):
                 ('created', models.DateTimeField(blank=True, default=django.utils.timezone.now, null=True)),
                 ('description', models.TextField(blank=True, null=True)),
                 ('counter', models.IntegerField(default=0, help_text='Counter for object_id asignment')),
-                ('authorized_groups', models.ManyToManyField(blank=True, related_name='authorized_prefix', to='auth.Group')),
+                ('public', models.BooleanField(default=True, help_text='Boolean field to indicate if there are restrictions on the use of this prefix')),
                 ('owner', models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, to=settings.AUTH_USER_MODEL, to_field='username')),
             ],
         ),

prefix/services.py

@@ -105,7 +105,12 @@ def create(self, validated_data):
         """
 
         validated_data.pop('user_permissions')
-        public = validated_data['public']
+
+        try: 
+            public = validated_data['public']
+        except KeyError:
+            public, validated_data['public'] = True, True
+
         prefix_instance = Prefix.objects.create(**validated_data, created=timezone.now())
 
         if public is False: